Ctrl+click or shift+click on the toolbar button to do a non-interactive choice of formats where your book has multiple. It will use the first found based on your preferred input format order list from Preferences->Behaviour

Could you make that last step be two options?
1) Run in non-interactive by default or interactive by default.
2) Follow preferred input format, or continue searching all if not found in first? I format down some of my epubs which is my preferred format.